Table 1

Overrepresented Gene Ontology attributes for genes with 5'UTR introns

N

X

LOD

P

P-adj

Gene Ontology attribute


25

35

0.650

1.4e-05

0.0153

GO:0004715:

non-membrane spanning protein tyrosine kinase activity

27

38

0.644

7.5e-06

0.0073

GO:0051261:

protein depolymerization

31

44

0.633

2.1e-06

0.0017

GO:0051494:

negative regulation of cytoskeleton organization and biogenesis

32

48

0.560

9.2e-06

0.0085

GO:0032956:

regulation of actin cytoskeleton organization and biogenesis

32

49

0.534

1.8e-05

0.0193

GO:0032970:

regulation of actin filament-based process

48

76

0.497

6.6e-07

0.0004

GO:0051493:

regulation of cytoskeleton organization and biogenesis

39

62

0.491

8.3e-06

0.0078

GO:0016459:

myosin complex

43

71

0.449

1.2e-05

0.0120

GO:0051129:

negative regulation of cellular component organization and biogenesis

51

88

0.404

1.1e-05

0.0114

GO:0033043:

regulation of organelle organization and biogenesis

105

216

0.243

3.5e-05

0.0398

GO:0015629:

actin cytoskeleton

1094

2356

0.232

5.7e-33

<0.0001

GO:0008270:

zinc ion binding

139

294

0.220

1.3e-05

0.0139

GO:0003779:

actin binding

996

2218

0.199

1.4e-23

<0.0001

GO:0006355:

regulation of transcription, DNA-dependent

1000

2233

0.197

3.4e-23

<0.0001

GO:0051252:

regulation of RNA metabolic process

1061

2380

0.195

7.5e-24

<0.0001

GO:0045449:

regulation of transcription

1013

2273

0.193

1.2e-22

<0.0001

GO:0006351:

transcription, DNA-dependent

1015

2277

0.193

9.5e-23

<0.0001

GO:0032774:

RNA biosynthetic process

191

420

0.190

8.3e-06

0.0077

GO:0008092:

cytoskeletal protein binding

1078

2436

0.189

6.6e-23

<0.0001

GO:0019219:

regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

1106

2512

0.185

1.3e-22

<0.0001

GO:0010468:

regulation of gene expression

1189

2713

0.183

1.6e-23

<0.0001

GO:0031323:

regulation of cellular metabolic process

1088

2477

0.182

8.6e-22

<0.0001

GO:0006350:

transcription

1211

2791

0.175

4.7e-22

<0.0001

GO:0019222:

regulation of metabolic process

989

2267

0.174

1.2e-18

<0.0001

GO:0003677:

DNA binding

1507

3515

0.172

2.9e-25

<0.0001

GO:0003676:

nucleic acid binding

1212

2825

0.165

5.5e-20

<0.0001

GO:0046914:

transition metal ion binding

1682

4053

0.147

1e-20

<0.0001

GO:0050794:

regulation of cellular process

1157

2784

0.136

5.6e-14

<0.0001

GO:0016070:

RNA metabolic process

1758

4305

0.134

3.7e-18

<0.0001

GO:0050789:

regulation of biological process

1772

4364

0.129

4.2e-17

<0.0001

GO:0005634:

nucleus

1463

3584

0.127

1.1e-14

<0.0001

GO:0006139:

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process


N represents the number of transcripts in the RefSeq collection that have both a 5'UTR intron and a given GO attribute; X represents the total number of transcripts having that GO attribute. For each attribute, P is the nominal P-value obtained from a one-tailed Fisher's Exact Test that calculates the probability that at least N transcripts have the particular attribute given the number of genes with 5'UTR introns. This nominal P-value is adjusted for multiple hypothesis testing to yield P-adj using a resampling approach that accounts for dependencies among the tested hypotheses (see [40] for precise procedure). The table is sorted in descending order by the log10 of the odds ratio (LOD score), where and M is the number of all genes, e is a pseudocount of 0.5 and q is the query set size. All attributes with LOD > 0.125 and a P-adj < 0.05 are reported.

Cenik et al. Genome Biology 2010 11:R29   doi:10.1186/gb-2010-11-3-r29

Open Data